The Cardinal's brother, Vincenzo Giustiniani, acquired an art collection of some 1600 items for the palace, including ancient statues and paintings by Giorgione, Titian, Raphael, and Caravaggio.

In 1859, with the extinction of the main line of the Giustiniani family, the palace became the property of the Grazioli, who leased it to the Grande Oriente d'Italia masonic order in 1898.

Litigation about this was resolved amicably in 1960 with an agreement between the society and Minister Giuseppe Trabucchi, which was proposed by US Secretary of State Christian Herter.

In 1972, the palace was mentioned as the place in which Aldo Moro and Amintore Fanfani (the President of the Senate at the time) made the "Pact of Palazzo Giustiniani" which delayed the passage of power to the younger generation of the Christian Democracy Party, in favour of their proteges, Ciriaco De Mita and Arnaldo Forlani, which effectively assured their rise to the head of the left and right wings (respectively) of the Christian Democracy party.

In 1973, the Communist parliamentarian and former mayor of Civita Castellana, Enrico Minio [it], committed suicide in his office in the palace, suffocating himself with a plastic bag.

The decorative cycle which dates to 1586–87, when the palace did not yet belong to the Giustiniani, is linked to Antonio Tempesta and Pietro Paolo Bonzi.